Profiles & Templates¶

Profiles and templates allow you to save and reuse complex configurations, making it easy to run repeated searches with consistent settings.

Profiles¶

What are Profiles?¶

Profiles save your command-line configuration (flags and their values) so you can reuse them without typing everything again.

Creating a Profile¶

Use --save-profile to save your current command configuration:

# Create a profile for Nature-style exports
lixplore -P -q "test" -X bibtex --sort newest -S first:20 --save-profile nature_style

# Create a profile for comprehensive searches
lixplore -A -q "test" -m 100 -D --enrich --sort newest --save-profile comprehensive

# Create a profile for quick PDF searches
lixplore -x -q "test" -m 50 --show-pdf-links --save-profile arxiv_pdfs

Using a Profile¶

Load a saved profile with --load-profile:

# Use the nature_style profile with a new query
lixplore -q "stem cells" --load-profile nature_style

# Use comprehensive profile
lixplore -q "quantum computing" --load-profile comprehensive

# Use arxiv_pdfs profile
lixplore -q "neural networks" --load-profile arxiv_pdfs

Listing Profiles¶

View all saved profiles:

lixplore --list-profiles

Output:

Saved Profiles:
1. nature_style
   - Sources: PubMed
   - Export: bibtex
   - Sort: newest
   - Selection: first:20

2. comprehensive
   - Sources: All
   - Max results: 100
   - Deduplicate: Yes
   - Enrich: Yes
   - Sort: newest

3. arxiv_pdfs
   - Sources: arXiv
   - Max results: 50
   - Show PDF links: Yes

Deleting a Profile¶

Remove a profile you no longer need:

lixplore --delete-profile nature_style

Profile Storage¶

Profiles are stored in:

~/.lixplore/profiles.json

You can back up this file to preserve your profiles.

Templates¶

What are Templates?¶

Templates are custom export format templates. While profiles save command configurations, templates customize how data is exported.

Available Templates¶

List all available templates:

lixplore --list-templates

Using a Template¶

Apply a template when exporting:

# Use a custom template
lixplore -P -q "research" -m 50 --template my_custom_template -X csv -o results.csv

Creating Custom Templates¶

Templates are stored in:

~/.lixplore/templates/

Create a custom template by adding a file there. For example, create ~/.lixplore/templates/minimal.txt:

{title}
{authors}
{year}
{doi}
---

Then use it:

lixplore -P -q "topic" -m 20 --template minimal

Common Profile Examples¶

Research Monitoring Profile¶

For daily monitoring of new research:

# Create the profile
lixplore -A -q "test" -m 50 -D --sort newest -S first:20 -X xlsx --save-profile daily_monitor

# Use daily with different topics
lixplore -q "COVID-19" --load-profile daily_monitor -o covid_daily.xlsx
lixplore -q "machine learning" --load-profile daily_monitor -o ml_daily.xlsx

Citation Export Profile¶

For exporting citations:

# Create profile
lixplore -P -q "test" -m 100 -X bibtex --sort year --save-profile citation_export

# Use for different topics
lixplore -q "neuroscience" --load-profile citation_export -o neuro.bib
lixplore -q "genomics" --load-profile citation_export -o genomics.bib

Comprehensive Review Profile¶

For literature reviews:

# Create profile with all features
lixplore -A -q "test" -m 500 -D --enrich --sort newest -S first:100 -X xlsx --save-profile lit_review

# Use for your review topic
lixplore -q "CRISPR applications" --load-profile lit_review -o crispr_review.xlsx

Open Access PDF Profile¶

For finding free PDFs:

# Create profile
lixplore -x -q "test" -m 100 --show-pdf-links --save-profile free_pdfs

# Use for different topics
lixplore -q "machine learning" --load-profile free_pdfs
lixplore -q "physics" --load-profile free_pdfs

Profile Best Practices¶

1. Name Profiles Descriptively¶

# Good names
--save-profile daily_covid_monitor
--save-profile bibtex_export_top50
--save-profile arxiv_pdfs_recent

# Poor names
--save-profile profile1
--save-profile temp
--save-profile test

2. Create Profiles for Repeated Tasks¶

If you run the same search pattern more than 3 times, create a profile for it.

3. Version Your Profiles¶

When updating a profile, create a new version:

lixplore ... --save-profile my_search_v2

4. Document Your Profiles¶

Keep a text file documenting what each profile does:

# Create a documentation file
cat > ~/.lixplore/profile_docs.txt << 'DOCS'
daily_monitor: Daily research monitoring, top 20 newest from all sources
citation_export: BibTeX export sorted by year
lit_review: Comprehensive review with 100 articles, enriched
free_pdfs: arXiv searches with PDF links
DOCS

5. Backup Your Profiles¶

# Backup profiles
cp ~/.lixplore/profiles.json ~/.lixplore/profiles_backup.json

# Or commit to version control
cd ~
git add .lixplore/profiles.json
git commit -m "Update lixplore profiles"

Combining Profiles with Other Features¶

Profiles + Automation¶

Use profiles in cron jobs:

# crontab -e
0 9 * * * lixplore -q "COVID-19 $(date +%Y)" --load-profile daily_monitor -o /home/user/covid_$(date +%Y%m%d).xlsx

Profiles + Annotations¶

Use profiles to search, then annotate:

# Search using profile
lixplore -q "interesting topic" --load-profile comprehensive

# Annotate important results
lixplore --annotate 5 --rating 5 --tags "important"

Profiles + Interactive Mode¶

Combine profiles with interactive browsing:

lixplore -q "research topic" --load-profile comprehensive -i

Profile Storage Format¶

Profiles are stored as JSON in ~/.lixplore/profiles.json:

{
  "nature_style": {
    "sources": ["pubmed"],
    "export_format": "bibtex",
    "sort": "newest",
    "selection": "first:20"
  },
  "comprehensive": {
    "sources": ["all"],
    "max_results": 100,
    "deduplicate": true,
    "enrich": true,
    "sort": "newest"
  }
}

You can manually edit this file if needed.

Troubleshooting¶

Profile not found¶

Error: Profile 'my_profile' not found

Solution: List available profiles with --list-profiles

Profile conflicts¶

If a profile has settings that conflict with command-line flags:

# Profile sets -m 100, but you also specify -m 50
lixplore -q "topic" -m 50 --load-profile my_profile

Command-line flags always override profile settings.

Corrupted profile file¶

If your profile file gets corrupted:

# Restore from backup
cp ~/.lixplore/profiles_backup.json ~/.lixplore/profiles.json

# Or delete and start fresh
rm ~/.lixplore/profiles.json

Export a Profile¶

# Copy profile to share with colleagues
cp ~/.lixplore/profiles.json ~/shared_profiles.json

Import a Profile¶

# Merge someone else's profiles with yours
# Manual merge required - edit ~/.lixplore/profiles.json

Team Profiles¶

For research teams, keep profiles in version control:

# In your project directory
mkdir .lixplore-profiles
cp ~/.lixplore/profiles.json .lixplore-profiles/team_profiles.json
git add .lixplore-profiles/
git commit -m "Add team search profiles"

Team members can then:

cp .lixplore-profiles/team_profiles.json ~/.lixplore/profiles.json

Summary¶

Profiles save command configurations for reuse
Templates customize export formats
Use --save-profile to create, --load-profile to use
List with --list-profiles, delete with --delete-profile
Perfect for automation and repeated searches
Store in ~/.lixplore/profiles.json

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